From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add bwa. Date: Thu, 12 Mar 2015 12:37:24 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58186) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YW1Qm-000280-Oe for guix-devel@gnu.org; Thu, 12 Mar 2015 07:37:37 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YW1Qi-00023Z-Vh for guix-devel@gnu.org; Thu, 12 Mar 2015 07:37:36 -0400 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:40161) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YW1Qi-00023M-It for guix-devel@gnu.org; Thu, 12 Mar 2015 07:37:32 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 7CD07280603 for ; Thu, 12 Mar 2015 12:37:30 +0100 (CET) Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id vilQ3ilsYjqZ for ; Thu, 12 Mar 2015 12:37:24 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Thu, 12 Mar 2015 12:37:24 +0100 (CET) List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel@gnu.org --=-=-= Content-Type: text/plain Hi Guix, here's a patch for an aligner tool: --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-bwa.patch" >From 6c03af7501c53c06a808906ce7d4fbd431bbf1ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 12 Mar 2015 12:35:14 +0100 Subject: [PATCH] gnu: Add bwa. * gnu/packages/bioinformatics.scm (bwa): New variable. --- gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 22ce71b..67326aa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -238,6 +238,53 @@ gapped, local, and paired-end alignment modes.") (supported-systems '("x86_64-linux")) (license license:gpl3+))) +(define-public bwa + (package + (name "bwa") + (version "0.7.12") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/bio-bwa/bwa-" + version ".tar.bz2")) + (sha256 + (base32 + "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh")))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ;no "check" target + #:phases + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append + (assoc-ref outputs "out") "/bin")) + (doc (string-append + (assoc-ref outputs "out") "/share/doc/bwa")) + (man (string-append + (assoc-ref outputs "out") "/share/man/man1"))) + (mkdir-p bin) + (mkdir-p doc) + (mkdir-p man) + (copy-file "bwa" (string-append bin "/bwa")) + (copy-file "README.md" (string-append doc "/README.md")) + (copy-file "bwa.1" (string-append man "/bwa.1")))) + ;; no "configure" script + (alist-delete 'configure %standard-phases)))) + (inputs `(("zlib" ,zlib))) + (home-page "http://bio-bwa.sourceforge.net/") + (synopsis "Burrows-Wheeler aligner") + (description + "BWA is a software package for mapping low-divergent sequences against a +large reference genome, such as the human genome. It consists of three +algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is +designed for Illumina sequence reads up to 100bp, while the rest two for +longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar +features such as long-read support and split alignment, but BWA-MEM, which is +the latest, is generally recommended for high-quality queries as it is faster +and more accurate. BWA-MEM also has better performance than BWA-backtrack for +70-100bp Illumina reads.") + (license license:gpl3))) + (define-public clipper (package (name "clipper") -- 2.1.0 --=-=-= Content-Type: text/plain The license is really just GPLv3; there are no license headers in the files that would imply otherwise and the only mention of the GPLv3 is in the README. ~~ Ricardo --=-=-=--